+Open data
-Basic information
Entry | Database: PDB / ID: 1ny3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ADP bound to MAP KAP kinase 2 | ||||||
Components | MAP kinase-activated protein kinase 2 | ||||||
Keywords | TRANSFERASE / MAP KAP kinase 2 / MK2 / ADP / kinase / ser/thr kinase | ||||||
Function / homology | Function and homology information macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / calcium-dependent protein serine/threonine kinase activity / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / mitogen-activated protein kinase binding ...macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / calcium-dependent protein serine/threonine kinase activity / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / regulation of interleukin-6 production / calcium/calmodulin-dependent protein kinase activity / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / Regulation of HSF1-mediated heat shock response / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / MAPK cascade / positive regulation of tumor necrosis factor production / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. ...Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Maguire, M. / Malakian, K. / Telliez, J.B. / Lin, L.L. / Kriz, R.W. / Seehra, J. / Somers, W.S. / Stahl, M.L. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Catalytically active MAP KAP kinase 2 structures in complex with staurosporine and ADP reveal differences with the autoinhibited enzyme Authors: Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Czerwinski, R.M. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Maguire, M. / Malakian, K. / ...Authors: Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Czerwinski, R.M. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Maguire, M. / Malakian, K. / Telliez, J.B. / Lin, L.L. / Kriz, R.W. / Seehra, J. / Somers, W.S. / Stahl, M.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ny3.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ny3.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ny3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ny3_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ny3_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 1ny3_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1ny3_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/1ny3 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/1ny3 | HTTPS FTP |
-Related structure data
Related structure data | 1nxkC 1nzkS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| x 12||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45629.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P49137, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
---|---|
#2: Chemical | ChemComp-ADP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.72 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 2.0M Ammonium Sulfate, pH unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2002 / Details: mirrors |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. all: 14402 / Num. obs: 14313 / % possible obs: 99.4 % / Redundancy: 6.96 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 21 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.29 / Num. unique all: 1385 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 3.1 Å / Num. obs: 12997 / % possible obs: 99.3 % / Num. measured all: 90852 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NZK Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.847 / SU B: 14.585 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.624 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.442 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.002→3.078 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.259 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|